Proteomic analysis of adipose tissue revealing differentially abundant proteins in highly efficient mid-lactating dairy cows

Arthur, P. F., Archer, J. A. & Herd, R. M. Feed intake and efficiency in beef cattle: Overview of recent Australian research and challenges for the future. Aust. J. Exp. Agric. 44, 361–369 (2004).
Google Scholar
Kelly, A. K. et al. Effect of divergence in residual feed intake on feeding behavior, blood metabolic variables, and body composition traits in growing beef heifers. J. Anim. Sci. 88, 109–123 (2010).
Google Scholar
Crowley, J. J. et al. Phenotypic and genetic parameters for different measures of feed efficiency in different breeds of Irish performance-tested beef bulls. J. Anim. Sci. 88, 885–894 (2010).
Google Scholar
Arthur, J. P. F. & Herd, R. M. Residual feed intake in beef cattle. Rev. Bras. Zootec. 37, 269–279 (2008).
Google Scholar
Herd, R. M., Oddy, V. H. & Richardson, E. C. Biological basis for variation in residual feed intake in beef cattle. 1. Review of potential mechanisms. Aust. J. Exp. Agric. 44, 423–430 (2004).
Google Scholar
Takiya, C. S. et al. Proteomic analysis reveals greater abundance of complement and inflammatory proteins in subcutaneous adipose tissue from postpartum cows treated with sodium salicylate. J. Proteom. 204, 103399 (2019).
Google Scholar
Contreras, G. A., Strieder-Barboza, C. & De Koster, J. Symposium review: Modulating adipose tissue lipolysis and remodeling to improve immune function during the transition period and early lactation of dairy cows. J. Dairy Sci. 101, 2737–2752 (2018).
Google Scholar
Faulkner, A. & Pollock, H. T. Metabolic responses to euglycaemic hyperinsulinaemia in lactating and non-lactating sheep in vivo. J. Endocrinol. 124, 59–66 (1990).
Google Scholar
De Koster, J. D. & Opsomer, G. Insulin resistance in dairy cows. Vet. Clin. Food Anim. Pract. 29, 299–322 (2013).
Google Scholar
Mukiibi, R. et al. Transcriptome analyses reveal reduced hepatic lipid synthesis and fat accumulation in more efficient beef cattle. Sci. Rep. 8, 7303 (2018).
Google Scholar
Alexandre, P. A. et al. Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle. BMC Genom. 16, 1073 (2015).
Google Scholar
Benedeti, P. D. B. et al. Nellore bulls (Bos taurus indicus) with high residual feed intake have increased the expression of genes involved in oxidative phosphorylation in rumen epithelium. Anim. Feed Sci. Technol. 235, 77–86 (2018).
Google Scholar
Khansefid, M. et al. Gene expression analysis of blood, liver, and muscle in cattle divergently selected for high and low residual feed intake1. J. Anim. Sci. 95, 4764–4775 (2017).
Google Scholar
Paradis, F. et al. Transcriptomic analysis by RNA sequencing reveals that hepatic interferon-in- duced genes may be associated with feed efficiency in beef heifers 1. J. Anim. Sci. 93, 3331–3341 (2015).
Google Scholar
Salleh, M. S. et al. RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle. BMC Genom. 18, 1–17 (2017).
Google Scholar
Tizioto, P. C. et al. Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes. BMC Genom. 16, 1–14 (2015).
Google Scholar
Tizioto, P. C. et al. Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake. Sci. Rep. 6, 1–12 (2016).
Google Scholar
Weber, K. L. et al. Identification of Gene networks for residual feed intake in Angus cattle using genomic prediction and RNA-seq. PLoS ONE 11, 1–19 (2016).
Zarek, C. M., Lindholm-Perry, A. K., Kuehn, L. A. & Freetly, H. C. Differential expression of genes related to gain and intake in the liver of beef cattle. BMC Res. Notes 10, 1–8 (2017).
Google Scholar
Bunnik, E. M. & Le Roch, K. G. An introduction to functional genomics and systems biology. Adv. Wound Care 2, 490–498 (2013).
Google Scholar
Berry, D. P. et al. The integration of omic disciplines and systems biology in cattle breeding. Animal 5, 493–505 (2011).
Google Scholar
Almeida, A. M. et al. Animal board invited review: Advances in proteomics for animal and food sciences. Animal 9, 1–17 (2015).
Google Scholar
Zachut, M. et al. Periparturient dairy cows do not exhibit hepatic insulin resistance, yet adipose-specific insulin resistance occurs in cows prone to high weight loss. J. Dairy Sci. 96, 5656–5669 (2013).
Google Scholar
Zachut, M. Defining the adipose tissue proteome of dairy cows to reveal biomarkers related to peripartum insulin resistance and metabolic status. J. Proteome Res. 14, 2863–2871 (2015).
Google Scholar
McNamara, J. P. & Huber, K. Metabolic and endocrine role of adipose tissue during lactation. Annu. Rev. Anim. Biosci. 6, 177–195 (2018).
Google Scholar
Piras, C. et al. Unraveling the adipose tissue proteome of transition cows through severe negative energy balance. Animals 9, 1013 (2019).
Google Scholar
McKenna, C. et al. An examination of skeletal muscle and hepatic tissue transcriptomes from beef cattle divergent for residual feed intake. Sci Rep 11, 8942. https://doi.org/10.1038/s41598-021-87842-3 (2021).
Google Scholar
Al-Husseini, W. et al. Expression of candidate genes for residual feed intake in Angus cattle. Anim. Genet. 45, 12–19 (2014).
Google Scholar
Ravi, S., Schilder, R. J. & Kimball, S. R. Role of precursor mRNA splicing in nutrient-induced alterations in gene expression and metabolism. J. Nutr. 145, 841–846 (2015).
Google Scholar
Joseph, S. B., Castrillo, A., Laffitte, B. A., Mangelsdorf, D. J. & Tontonoz, P. Reciprocal regulation of inflammation and lipid metabolism by liver X receptors. Nat. Med. 9, 213–219 (2003).
Google Scholar
Fowler, A. J. et al. Liver X receptor activators display anti-inflammatory activity in irritant and allergic contact dermatitis models: liver-X-receptor-specific inhibition of inflammation and primary cytokine production. J. Invest. Dermatol. 120, 246–255 (2003).
Google Scholar
Zhou, N., Lee, W. R. & Abasht, B. Messenger RNA sequencing and pathway analysis provide novel insights into the biological basis of chickens’ feed efficiency. BMC Genom. 16, 195 (2015).
Google Scholar
Kong, B.-W. et al. RNA sequencing for global gene expression associated with muscle growth in a single male modern broiler line compared to a foundational barred plymouth rock chicken line. BMC Genom. 18, 82 (2017).
Google Scholar
Dorji, J. et al. Mitochondrial protein gene expression and the oxidative phosphorylation pathway associated with feed efficiency and energy balance in dairy cattle. J. Dairy Sci. 104, 575–587 (2021).
Google Scholar
Swartz, T. H. et al. Characterization of the liver proteome in dairy cows experiencing negative energy balance at early lactation. J. Proteom. 246, 104308 (2021).
Google Scholar
Sierżant, K., Perruchot, M.-H., Merlot, E., Le Floc’h, N. & Gondret, F. Tissue-specific responses of antioxidant pathways to poor hygiene conditions in growing pigs divergently selected for feed efficiency. BMC Vet. Res. 15, 341 (2019).
Google Scholar
Kelly, A. K. et al. mRNA expression of genes regulating oxidative phosphorylation in the muscle of beef cattle divergently ranked on residual feed intake. Physiol. Genom. 43, 12–23 (2011).
Google Scholar
Iqbal, M. et al. Low feed efficient broilers within a single genetic line exhibit higher oxidative stress and protein expression in breast muscle with lower mitochondrial complex activity. Poult. Sci. 83, 474–484 (2004).
Google Scholar
Kong, R. S. G., Liang, G., Chen, Y., Stothard, P. & Guan, L. L. Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake. BMC Genom. 17, 592 (2016).
Google Scholar
Lindholm-Perry, A. K. et al. Profile of the spleen transcriptome in beef steers with variation in gain and feed intake. Front. Genet. 7, 127 (2016).
Google Scholar
Santana, M. H. A. et al. Systems genetics investigations for feed intake, feed efficiency and performance in Nellore (Bos indicus) Cattle. In Proceedings of the 10th World Congress of Genetics Applied to Livestock Production. Auckland, 11–18th February (2018).
Dekker, S. L., Kampinga, H. H. & Bergink, S. DNAJs: more than substrate delivery to HSPA. Front. Mol. Biosci. 2, 35 (2015).
Google Scholar
Chen, Y. et al. Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake. Anim. Genet. 42, 475–490 (2011).
Google Scholar
Keogh, K., Kenny, D. A., Cormican, P., Kelly, A. K. & Waters, S. M. Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of hepatic tissue in cattle. BMC Genom. 17, 244 (2016).
Google Scholar
Dowhan, D. H. et al. Steroid hormone receptor coactivation and alternative RNA splicing by U2AF65-related proteins CAPERα and CAPERβ. Mol. Cell 17, 429–439 (2005).
Google Scholar
Morandi, E. M. et al. ITGAV and ITGA5 diversely regulate proliferation and adipogenic differentiation of human adipose derived stem cells. Sci. Rep. 6, 1–14 (2016).
Google Scholar
Harp, J. B., Franklin, D., Vanderpuije, A. A. & Gimble, J. M. Differential expression of signal transducers and activators of transcription during human adipogenesis. Biochem. Biophys. Res. Commun. 281, 907–912 (2001).
Google Scholar
Ben Meir, Y. A. et al. Eating behavior, milk production, rumination, and digestibility characteristics of high-and low-efficiency lactating cows fed a low-roughage diet. J. Dairy Sci. 101, 10973–10984 (2018).
Google Scholar
Asher, A. et al. Time required to determine performance variables and production efficiency of lactating dairy cows. J. Dairy Sci. 97, 4340–4353 (2014).
Google Scholar
Ben Meir, Y. A. et al. Effect of lactation trimester and parity on eating behavior, milk production and efficiency traits of dairy cows. Animal 13, 1736–1743 (2019).
Google Scholar
Moallem, U. Future consequences of decreasing marginal production efficiency in the high-yielding dairy cow. J. Dairy Sci. 99, 2986–2995 (2016).
Google Scholar
Zachut, M., Sood, P., Levin, Y. & Moallem, U. Proteomic analysis of preovulatory follicular fluid reveals differentially abundant proteins in less fertile dairy cows. J. Proteom. 139, 122–129 (2016).
Google Scholar
Zachut, M. et al. Proteome dataset of subcutaneous adipose tissue obtained from late pregnant dairy cows during summer heat stress and winter seasons. Data Br. 12, 535–539 (2017).
Google Scholar
Feldman, E. Animal models of diabetic complications consortium (AMDCC protocols). Version 1, 1–3 (2004).
Shalit, T., Elinger, D., Savidor, A., Gabashvili, A. & Levin, Y. MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer. J. Proteome Res. 14, 1979–1986 (2015).
Google Scholar
Daddam, J. R., Sreenivasulu, B., Peddanna, K. & Umamahesh, K. Designing, docking and molecular dynamics simulation studies of novel cloperastine analogues as anti-allergic agents: Homology modeling and active site prediction for the human histamine H1 receptor. RSC Adv. 10, 4745–4754 (2020).
Google Scholar
Jeanmougin, F., Thompson, J. D., Gouy, M., Higgins, D. G. & Gibson, T. J. Multiple sequence alignment with clustal X. Trends Biochem. Sci. 23, 403–405 (1998).
Google Scholar
Daddam, J. R., Sreenivasulu, B., Umamahesh, K., Peddanna, K. & Rao, D. M. In silico studies on anti-stress compounds of ethanolic root extract of hemidesmus indicus L. Curr. Pharm. Biotechnol. 21, 502–515 (2020).
Google Scholar
Šali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779–815 (1993).
Google Scholar
Phillips, J. C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 44130 (2020).
Google Scholar
Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993).
Google Scholar
Sura, M. & Daddam, J. R. Structure prediction, molecular simulations of RmlD from Mycobacterium tuberculosis, and interaction studies of Rhodanine derivatives for anti-tuberculosis activity. J. Mol. Model. 27, 75 (2021).
Google Scholar
Kurjogi, M. et al. Computational modeling of the staphylococcal enterotoxins and their interaction with natural antitoxin compounds. Int. J. Mol. Sci. 19, 133 (2018).
Google Scholar
Kra, G., Daddam, J. R., Gabay, H., Yosefi, S. & Zachut, M. Antioxidant resveratrol increases li polytic and reduces lipogenic gene expression under in vitro heat stress conditions in dedifferentiated adipocyte-derived progeny cells from dairy cows. Antioxidants 10, 905 (2021).
Google Scholar